Ancient Noncoding Elements Conserved in the Human Genome
Abstract
Cartilaginous fishes represent the living group of jawed vertebrates that diverged from the common ancestor of human and teleost fish lineages about 530 million years ago. We generated ~1.4× genome sequence coverage for a cartilaginous fish, the elephant shark (Callorhinchus milii), and compared this genome with the human genome to identify conserved noncoding elements (CNEs). The elephant shark sequence revealed twice as many CNEs as were identified by whole-genome comparisons between teleost fishes and human. The ancient vertebrate-specific CNEs in the elephant shark and human genomes are likely to play key regulatory roles in vertebrate gene expression.
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References
1
S. Kumar, S. B. Hedges, Nature392, 917 (1998).
2
J. T. Shin et al., Nucleic Acids Res.33, 5437 (2005).
3
A. Woolfe et al., PLoS Biol.3, e7 (2005).
4
B. Venkatesh, A. Tay, N. Dandona, J. G. Patil, S. Brenner, Curr. Biol.15, R82 (2005).
5
C. H. Chiu et al., Proc. Natl. Acad. Sci. U.S.A.99, 5492 (2002).
6
A. Christoffels et al., Mol. Biol. Evol.21, 1146 (2004).
7
J. Postlethwait, A. Amores, W. Cresko, A. Singer, Y. L. Yan, Trends Genet.20, 481 (2004).
8
This project was supported by the Agency for Science, Technology, and Research (A*STAR), Singapore. We thank J. G. Patil for help in collecting the elephant shark and the Sanger Institute for making available the zebrafish assembly for comparative analysis. A.P.L. is supported by the A*STAR Graduate Scholarship. B.V. is an adjunct staff of the Department of Pediatrics, Yong Loo Lin School of Medicine, National University of Singapore.
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Published In
Science
Volume 314 | Issue 5807
22 December 2006
22 December 2006
Copyright
American Association for the Advancement of Science.
Submission history
Received: 1 June 2006
Accepted: 27 October 2006
Published in print: 22 December 2006
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